RNA-Seq-Based Transcript Structure Analysis with TrBorderExt

Abstract Motivation High-throughput RNA sequencing has revolutionized the scope and depth of transcriptome analysis. Accurate reconstruction of a phenotype-specific transcriptome is challenging due to the noise and variability of RNA-seq data. This requires computational identification of transcripts from multiple samples of the same phenotype, given the underlying consensus transcript structure. Results We present a Bayesian method, integrated assembly of phenotype-specific transcripts (IntAPT), that identifies phenotype-specific isoforms from multiple RNA-seq profiles. IntAPT features a novel two-layer Bayesian model to capture the presence of isoforms at the group layer and to quantify the abundance of isoforms at the sample layer. A spike-and-slab prior is used to model the isoform expression and to enforce the sparsity of expressed isoforms. Dependencies between the existence of isoforms and their expression are modeled explicitly to facilitate parameter estimation. Model parameters are estimated iteratively using Gibbs sampling to infer the joint posterior distribution, from which the presence and abundance of isoforms can reliably be determined. Studies using both simulations and real datasets show that IntAPT consistently outperforms existing methods for the IntAPT. Experimental results demonstrate that, despite sequencing errors, IntAPT exhibits a robust performance among multiple samples, resulting in notably improved identification of expressed isoforms of low abundance. Availability and implementation The IntAPT package is available at http://github.com/henryxushi/IntAPT. Supplementary information Supplementary data are available at Bioinformatics online.

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200kv superconducting cryo electron microscope

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100127645 ◽

1987 ◽

Vol 45 ◽

pp. 642-643

Author(s):

M. Iwatsuki ◽

Y. Kokubo ◽

Y. Harada ◽

J. Lehman

Keyword(s):

Electron Microscope ◽

Structure Analysis ◽

Organic Materials ◽

Strong Interactions ◽

Specimen Preparation ◽

Great Effort ◽

Electron Microscopic ◽

Crystal Fields ◽

Special Skill ◽

Long Time

In recent years, the electron microscope has been significantly improved in resolution and we can obtain routinely atomic-level high resolution images without any special skill. With this improvement, the structure analysis of organic materials has become one of the interesting targets in the biological and polymer crystal fields.Up to now, X-ray structure analysis has been mainly used for such materials. With this method, however, great effort and a long time are required for specimen preparation because of the need for larger crystals. This method can analyze average crystal structure but is insufficient for interpreting it on the atomic or molecular level. The electron microscopic method for organic materials has not only the advantage of specimen preparation but also the capability of providing various information from extremely small specimen regions, using strong interactions between electrons and the substance. On the other hand, however, this strong interaction has a big disadvantage in high radiation damage.

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